GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglF in Synechococcus elongatus PCC 7942

Align ABC transporter for D-Maltose and D-Trehalose, permease component 1 (characterized)
to candidate Synpcc7942_0526 Synpcc7942_0526 ABC-type sugar transport systems permease components-like

Query= reanno::Smeli:SMc03062
         (336 letters)



>FitnessBrowser__SynE:Synpcc7942_0526
          Length = 293

 Score =  123 bits (309), Expect = 5e-33
 Identities = 78/243 (32%), Positives = 127/243 (52%), Gaps = 16/243 (6%)

Query: 49  IANSIRPWLFLAPALLALTLYLVYPVVQSVWLSL-----HGRGGQNFVGLSNYSWMINDG 103
           + + + P+LFLAPAL  L L + +P +Q+ + S      +      +VGL N+  ++ND 
Sbjct: 4   LRDRLSPYLFLAPALTILGLTVFWPALQAFYFSFTRFDYNLTRSPQWVGLENFQRLLNDA 63

Query: 104 EFRQSIFNNFLWLLVVPALSTFFGLIIAALTDRIWWG-NIAKTLIFMPMAISFVGAAVIW 162
            F +++ N F++L+ V  L  F  L +A L +R   G  + +   + P+ +S V A + W
Sbjct: 64  VFWKTLGNTFIYLIGVVPLLVFLPLGLAILVNRPLRGITLFRLAYYTPVIVSIVVAGIAW 123

Query: 163 KFIYDYRAAGSEQIGLLNAI---VVALGGEPQAWITLPFWNNFFLMVILIWIQTGFAMVI 219
           +++Y        + GLLN +   V   G +P  W+T P    F +M + +W   G+ MVI
Sbjct: 124 RWLY-------AETGLLNQLGQLVFGEGFQPIPWLTSPALALFSVMAVTVWKGLGYYMVI 176

Query: 220 LSAALRGIPEETIEAAVIDGANGWQIFFKIMVPQIWGTIAVVWTTITILVLKVFDIVLAM 279
             A L+GIP E  EAA +DG++GW+    I +P +   + +V     I   KVF+ V  M
Sbjct: 177 YLAGLQGIPLELYEAAALDGSDGWRRHLDITLPLMRPYLVLVAVISAISATKVFEEVFIM 236

Query: 280 TNG 282
           T G
Sbjct: 237 TQG 239


Lambda     K      H
   0.330    0.142    0.466 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 261
Number of extensions: 9
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 336
Length of database: 293
Length adjustment: 27
Effective length of query: 309
Effective length of database: 266
Effective search space:    82194
Effective search space used:    82194
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory